Error in prep_call_sampler(object)

General
1

H all,

I’m getting a rather strange error that I have not received in earlier analyses of exactly the same code and data. The error message reads

Error in prep_call_sampler(object) : the compiled object from C++ code for this model is invalid, possible reasons: - compiled with save_dso=FALSE; - compiled on a different platform; - does not exist (created from reading csv files).

Here is the code

modelString ="
data {
int <lower=0> n;
vector[n] age;
vector[n] male;
int <lower=0,upper=1> chd[n];
}
parameters {
real alpha;
real beta1;
real beta2;
}

transformed parameters {
real <lower=0> oddsbeta1;
real <lower=0> oddsbeta2;

oddsbeta1 = exp(beta1);
oddsbeta2 = exp(beta2);

}

model {
for (i in 1:n) {
chd[i] ~ bernoulli_logit(alpha + beta1age[i] + beta2male[i]);
}

// Priors
alpha ~ normal(0, 1);
beta1 ~ normal(0, 1);
beta2 ~ normal(0, 1);
}

generated quantities {
real chd_rep[n];
vector[n] log_lik;
for (i in 1:n) {
chd_rep[i] = bernoulli_logit_rng(alpha + beta1age[i] + beta2male[i]);
log_lik[i] = bernoulli_logit_lpmf(chd[i] | alpha + beta1age[i] +
beta2male[i]);
}

}
"

# Start estimation
```{r, echo=TRUE}
nChains = 3
nIter= 30000
thinSteps = 10
burnInSteps = floor(nIter/2)


myfitCHD = stan(data=data.list,model_code=modelString,chains=nChains,
              iter=nIter,warmup=burnInSteps,thin=thinSteps)


Thanks in advance,

David
2

Hi David,

Do you get the same error if you run the code above in a fresh R session with no other models loaded in?

Also, can you post the output from the following:

devtools::session_info("rstan")
1 Like
3

Strangely enough, clearing out all of the other models did the trick. Also, it seems that knitting the whole markdown code is better than running the analysis one chunk at a time. Mysterious. Thanks!

David